Multiscale modeling of diffusion in a crowded environment
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Abstract: We present a multiscale approach to model diffusion in a crowded environment and its effect on the reaction rates. Diffusion in biological systems is often modeled by a discrete space jump process in order to capture the inherent noise of biological systems, which becomes important in the low copy number regime. To model diffusion in the crowded cell environment efficiently, we compute the jump rates in this mesoscopic model from local first exit times, which account for the microscopic positions of the crowding molecules, while the diffusing molecules jump on a coarser Cartesian grid. We then extract a macroscopic description from the resulting jump rates, where the excluded volume effect is modeled by a diffusion equation with space dependent diffusion coefficient. The crowding molecules can be of arbitrary shape and size and numerical experiments demonstrate that those factors together with the size of the diffusing molecule play a crucial role on the magnitude of the decrease in diffusive motion. When correcting the reaction rates for the altered diffusion we can show that molecular crowding either enhances or inhibits chemical reactions depending on local fluctuations of the obstacle density.
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Cited in
(10)- Brownian dynamics simulation of macromolecule diffusion in a protocell
- Micro- and macroscopic modeling of crowding and pushing in corridors
- Modeling transport through an environment crowded by a mixture of obstacles of different shapes and sizes
- Facilitated diffusion in a crowded environment: from kinetics to stochastics
- An explicit numerical scheme to efficiently simulate molecular diffusion in environments with dynamically changing barriers
- Monte Carlo simulations of enzymatic reactions in crowded media. Effect of the enzyme-obstacle relative size
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- scientific article; zbMATH DE number 5954683 (Why is no real title available?)
- Optimal cytoplasmatic density and flux balance model under macromolecular crowding effects
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